Download MendeleyProbing the role of aromatic residues
Ragunath, C., A Manuel, S.G., Sait, H.M., Kasinathan, C., Ramasubbu, N.To be published.
3DHP
Probing the role of aromatic residues at the secondary saccharide binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding
- PDB DOI: https://doi.org/10.2210/pdb3DHP/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes
- Deposited: 2008-06-18 Released: 2008-07-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 ?
- R-Value Free: 0.186
- R-Value Work: 0.169
- R-Value Observed: 0.170
Starting Model: experimental
View more details
This is version 3.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Alpha-amylase 1 | 496 | Homo sapiens | Mutation(s): 6 EC: 3.2.1.1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0DUB6 (Homo sapiens) Explore P0DUB6 Go to UniProtKB: P0DUB6 | |||||
GTEx: ENSG00000237763 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DUB6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GLC Query on GLC | C [auth A] | alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N |  | ||
| HMC Query on HMC | F [auth A] | 5-HYDROXYMETHYL-CHONDURITOL C7 H12 O5 PJPGMULJEYSZBS-VZFHVOOUSA-N |  | ||
| CA Query on CA | D [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PCA Query on PCA | A | L-PEPTIDE LINKING | C5 H7 N O3 |  | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 ?
- R-Value Free: 0.186
- R-Value Work: 0.169
- R-Value Observed: 0.170
- Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 52.736 | ¦Á = 90 |
| b = 73.722 | ¦Â = 90 |
| c = 134.095 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2008-07-01 Deposition Author(s): Ragunath, C., Manuel, S.G.A., Sait, H.M., Kasinathan, C.
Revision History (Full details and data files)
- Version 1.0: 2008-07-01
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2018-01-24
Changes: Structure summary - Version 2.0: 2019-12-25
Changes: Data collection, Database references, Derived calculations, Polymer sequence - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2021-10-20
Changes: Database references, Derived calculations, Structure summary - Version 3.2: 2023-08-30
Changes: Data collection, Refinement description - Version 3.3: 2024-11-06
Changes: Structure summary
